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Fix for Solid reads that have '.' in their color space field. The recalibrator will just set them to be illumina reads and won't apply color space correction. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2661 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-22 20:09:16 +00:00
parent 2ea768d902
commit 7732f98e56
1 changed files with 9 additions and 1 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
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@ -259,12 +259,16 @@ public class RecalDataManager {
if( attr != null ) { if( attr != null ) {
char[] colorSpace; char[] colorSpace;
if( attr instanceof String ) { if( attr instanceof String ) {
if( ((String)attr).contains(".") ) { // empty color space, abort
read.getReadGroup().setPlatform("illumina");
return;
}
colorSpace = ((String)attr).toCharArray(); colorSpace = ((String)attr).toCharArray();
} else { } else {
throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName())); throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
} }
// Loop over the read and calculate first the infered bases from the color and then check if it is consistent with the read // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read
byte[] readBases = read.getReadBases(); byte[] readBases = read.getReadBases();
if( read.getReadNegativeStrandFlag() ) { if( read.getReadNegativeStrandFlag() ) {
readBases = BaseUtils.simpleReverseComplement( read.getReadBases() ); readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
@ -304,6 +308,10 @@ public class RecalDataManager {
if( attr != null ) { if( attr != null ) {
char[] colorSpace; char[] colorSpace;
if( attr instanceof String ) { if( attr instanceof String ) {
if( ((String)attr).contains(".") ) { // empty color space, abort
read.getReadGroup().setPlatform("illumina");
return originalQualScores;
}
colorSpace = ((String)attr).toCharArray(); colorSpace = ((String)attr).toCharArray();
} else { } else {
throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName())); throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));